Remove usage of "logger" and un-necessary comments wrt the same

Logging is used to introspect variables or notify the commencement of
a given operation.  Logging should only be used to log errors.  Also,
most of the logging is either "logger.debug" or "logger.info"; and
this won't show up in production/testing since we need a logging level
above "WARNING" for them to show up.

* wqflask/base/data_set.py (create_datasets_list): Remove logger.
(Markers.add_pvalues): Ditto.
(DataSet.retrieve_other_names): Ditto.
* wqflask/base/mrna_assay_tissue_data.py: Ditto.
* wqflask/base/webqtlCaseData.py: Ditto.
* wqflask/db/call.py (fetch1): Ditto.
(gn_server): Ditto.
* wqflask/db/gn_server.py: Ditto.
* wqflask/maintenance/set_resource_defaults.py: Ditto.
* wqflask/utility/Plot.py (find_outliers): Ditto.
* wqflask/utility/gen_geno_ob.py: Ditto.
* wqflask/utility/helper_functions.py: Ditto.
* wqflask/utility/pillow_utils.py: Ditto.
* wqflask/utility/redis_tools.py: Ditto.
* wqflask/wqflask/api/gen_menu.py (get_groups): Ditto.
* wqflask/wqflask/api/mapping.py: Ditto.
* wqflask/wqflask/api/router.py (get_dataset_info): Ditto.
* wqflask/wqflask/collect.py (report_change): Ditto.
* wqflask/wqflask/correlation/corr_scatter_plot.py: Ditto.
* wqflask/wqflask/ctl/ctl_analysis.py (CTL): Ditto.
(CTL.__init__): Ditto.
(CTL.run_analysis): Ditto.
(CTL.process_results): Ditto.
* wqflask/wqflask/db_info.py: Ditto.
* wqflask/wqflask/do_search.py (DoSearch.execute): Ditto.
(DoSearch.mescape): Ditto.
(DoSearch.get_search): Ditto.
(MrnaAssaySearch.run_combined): Ditto.
(MrnaAssaySearch.run): Ditto.
(PhenotypeSearch.run_combined): Ditto.
(GenotypeSearch.get_where_clause): Ditto.
(LrsSearch.get_where_clause): Ditto.
(MeanSearch.run): Ditto.
(RangeSearch.get_where_clause): Ditto.
(PvalueSearch.run): Ditto.
* wqflask/wqflask/docs.py: Ditto.
* wqflask/wqflask/export_traits.py: Ditto.
* wqflask/wqflask/external_tools/send_to_bnw.py: Ditto.
* wqflask/wqflask/external_tools/send_to_geneweaver.py: Ditto.
* wqflask/wqflask/external_tools/send_to_webgestalt.py: Ditto.
* wqflask/wqflask/gsearch.py (GSearch.__init__): Ditto.
* wqflask/wqflask/heatmap/heatmap.py: Ditto.
* wqflask/wqflask/marker_regression/display_mapping_results.py (DisplayMappingResults): Ditto.
* wqflask/wqflask/marker_regression/gemma_mapping.py: Ditto.
* wqflask/wqflask/marker_regression/plink_mapping.py (run_plink): Ditto.
* wqflask/wqflask/marker_regression/qtlreaper_mapping.py (run_reaper): Ditto.
* wqflask/wqflask/marker_regression/rqtl_mapping.py: Ditto.
* wqflask/wqflask/marker_regression/run_mapping.py (RunMapping.__init__): Ditto.
* wqflask/wqflask/parser.py (parse): Ditto.
* wqflask/wqflask/search_results.py (SearchResultPage.__init__): Ditto.
* wqflask/wqflask/update_search_results.py (GSearch.__init__): Ditto.
* wqflask/wqflask/user_login.py (send_email): Ditto.
(logout): Ditto.
(forgot_password_submit): Ditto.
(password_reset): Ditto.
(password_reset_step2): Ditto.
(register): Ditto.
* wqflask/wqflask/user_session.py (create_signed_cookie): Ditto.

36 files changed, 2 insertions, 189 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 211c6752..8206b67c 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -22,7 +22,6 @@ from dataclasses import field
 from dataclasses import InitVar
 from typing import Optional, Dict, List
 from db.call import fetchall, fetchone, fetch1
-from utility.logger import getLogger
 from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL
 from db.gn_server import menu_main
 from pprint import pformat as pf
@@ -60,8 +59,6 @@ from redis import Redis
 
 r = Redis()
 
-logger = getLogger(__name__)
-
 # Used by create_database to instantiate objects
 # Each subclass will add to this
 DS_NAME_MAP = {}
@@ -200,7 +197,6 @@ def create_datasets_list():
         result = r.get(key)
 
         if result:
-            logger.debug("Redis cache hit")
             datasets = pickle.loads(result)
 
     if result is None:
@@ -213,10 +209,6 @@ def create_datasets_list():
             for dataset_type in type_dict:
                 query = "SELECT Name FROM {}".format(type_dict[dataset_type])
                 for result in fetchall(query):
-                    # The query at the beginning of this function isn't
-                    # necessary here, but still would rather just reuse
-                    # it logger.debug("type: {}\tname:
-                    # {}".format(dataset_type, result.Name))
                     dataset = create_dataset(result.Name, dataset_type)
                     datasets.append(dataset)
 
@@ -259,9 +251,6 @@ class Markers:
         self.markers = markers
 
     def add_pvalues(self, p_values):
-        logger.debug("length of self.markers:", len(self.markers))
-        logger.debug("length of p_values:", len(p_values))
-
         if isinstance(p_values, list):
             # THIS IS only needed for the case when we are limiting the number of p-values calculated
             # if len(self.markers) > len(p_values):
@@ -664,8 +653,6 @@ class DataSet:
                     """ % (query_args))
 
         except TypeError:
-            logger.debug(
-                "Dataset {} is not yet available in GeneNetwork.".format(self.name))
             pass
 
     def chunk_dataset(self, dataset, n):
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index 8f8e2b0a..d7e747aa 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -9,10 +9,6 @@ from utility.db_tools import escape
 from gn3.db_utils import database_connector
 
 
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
-
 class MrnaAssayTissueData:
 
     def __init__(self, gene_symbols=None):
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index 25b6cb8a..dd6fad04 100644
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -21,9 +21,6 @@
 # Created by GeneNetwork Core Team 2010/08/10
 
 
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
 import utility.tools
 
 utility.tools.show_settings()
diff --git a/wqflask/db/call.py b/wqflask/db/call.py
index 1fe0772b..a6bbda54 100644
--- a/wqflask/db/call.py
+++ b/wqflask/db/call.py
@@ -31,9 +31,6 @@ GN_SERVER result when set (which should return a Tuple)
             res2 = func(result)
         else:
             res2 = result,
-        if LOG_SQL:
-            logger.debug("Replaced SQL call", query)
-        logger.debug(path, res2)
         return res2
     else:
         return fetchone(query)
@@ -75,5 +72,4 @@ def gn_server(path):
             res = urllib2.urlopen(GN_SERVER_URL + path)
         rest = res.read()
         res2 = json.loads(rest)
-        logger.debug(res2)
         return res2
diff --git a/wqflask/db/gn_server.py b/wqflask/db/gn_server.py
index f9b01658..af6682ba 100644
--- a/wqflask/db/gn_server.py
+++ b/wqflask/db/gn_server.py
@@ -2,9 +2,6 @@
 
 from db.call import gn_server
 
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
 
 def menu_main():
     return gn_server("/int/menu/main.json")
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index 22d73ba3..0d9372ff 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -33,8 +33,6 @@ Redis = get_redis_conn()
 import urllib.parse
 
 from wqflask.database import database_connection
-from utility.logger import getLogger
-logger = getLogger(__name__)
 
 
 def parse_db_uri():
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index d4256a46..df7156b4 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -33,8 +33,7 @@ from math import *
 import utility.corestats as corestats
 from base import webqtlConfig
 from utility.pillow_utils import draw_rotated_text
-import utility.logger
-logger = utility.logger.getLogger(__name__)
+
 
 # ---- Define common colours ---- #
 BLUE = ImageColor.getrgb("blue")
@@ -105,7 +104,6 @@ def find_outliers(vals):
     """
 
     if vals:
-        #logger.debug("vals is:", pf(vals))
         stats = corestats.Stats(vals)
         low_hinge = stats.percentile(25)
         up_hinge = stats.percentile(75)
diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py
index e619b7b6..c7a1ea59 100644
--- a/wqflask/utility/gen_geno_ob.py
+++ b/wqflask/utility/gen_geno_ob.py
@@ -1,7 +1,3 @@
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
-
 class genotype:
     """
     Replacement for reaper.Dataset so we can remove qtlreaper use while still generating mapping output figure
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index 27dd0729..4229a91f 100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -6,9 +6,6 @@ from utility import hmac
 
 from flask import g
 
-import logging
-logger = logging.getLogger(__name__)
-
 
 def get_species_dataset_trait(self, start_vars):
     if "temp_trait" in list(start_vars.keys()):
diff --git a/wqflask/utility/pillow_utils.py b/wqflask/utility/pillow_utils.py
index 5713e155..e302df18 100644
--- a/wqflask/utility/pillow_utils.py
+++ b/wqflask/utility/pillow_utils.py
@@ -2,9 +2,6 @@ from PIL import Image, ImageColor, ImageDraw, ImageFont
 
 from utility.tools import TEMPDIR
 
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
 BLACK = ImageColor.getrgb("black")
 WHITE = ImageColor.getrgb("white")
 
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index 641d973e..945efbbd 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -5,8 +5,6 @@ import datetime
 import redis  # used for collections
 
 from utility.hmac import hmac_creation
-from utility.logger import getLogger
-logger = getLogger(__name__)
 
 
 def get_redis_conn():
diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py
index 5d239343..45d5739e 100644
--- a/wqflask/wqflask/api/gen_menu.py
+++ b/wqflask/wqflask/api/gen_menu.py
@@ -1,8 +1,5 @@
 from gn3.db.species import get_all_species
 
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
 def gen_dropdown_json(conn):
     """Generates and outputs (as json file) the data for the main dropdown menus on
     the home page
@@ -31,7 +28,6 @@ def get_groups(species, conn):
                  "InbredSet.FullName) ASC, IFNULL(InbredSet.Family, "
                  "InbredSet.FullName) ASC, InbredSet.FullName ASC, "
                  "InbredSet.MenuOrderId ASC").format(species_name)
-            # logger.debug(query)
             cursor.execute(query)
             results = cursor.fetchall()
             for result in results:
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index 3d33cc87..95cd2953 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -25,8 +25,6 @@ from utility.tools import flat_files
 
 from wqflask.database import database_connection
 
-import utility.logger
-logger = utility.logger.getLogger(__name__)
 
 version = "pre1"
 
@@ -275,8 +273,6 @@ def get_dataset_info(dataset_name, group_name=None, file_format="json"):
                                InbredSet.Name = "{0}" AND PublishXRef.Id = "{1}"
                       """.format(group_name, dataset_name)
 
-        logger.debug("QUERY:", pheno_query)
-
         pheno_results = g.db.execute(pheno_query)
         dataset = pheno_results.fetchone()
 
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 891da437..bb0973d5 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -21,9 +21,7 @@ from base.trait import retrieve_trait_info
 from base.trait import jsonable
 from base.data_set import create_dataset
 
-from utility.logger import getLogger
 
-logger = getLogger(__name__)
 Redis = get_redis_conn()
 
 
@@ -48,8 +46,6 @@ def report_change(len_before, len_now):
     if new_length:
         flash("We've added {} to your collection.".format(
             numify(new_length, 'new trait', 'new traits')))
-    else:
-        logger.debug("No new traits were added.")
 
 
 @app.route("/collections/store_trait_list", methods=('POST',))
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index cafb9265..5df28c45 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -8,9 +8,6 @@ from utility import corr_result_helpers
 from scipy import stats
 import numpy as np
 
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
 
 class CorrScatterPlot:
     """Page that displays a correlation scatterplot with a line fitted to it"""
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index bb928ec5..96a47eb8 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -24,8 +24,6 @@ from utility.tools import locate, GN2_BRANCH_URL
 
 from rpy2.robjects.packages import importr
 
-import utility.logger
-logger = utility.logger.getLogger(__name__)
 
 # Get pointers to some common R functions
 r_library = ro.r["library"]             # Map the library function
@@ -42,14 +40,9 @@ r_as_numeric = ro.r["as.numeric"]         # Map the write.table function
 
 class CTL:
     def __init__(self):
-        logger.info("Initialization of CTL")
-        #log = r_file("/tmp/genenetwork_ctl.log", open = "wt")
-        # r_sink(log)                                                       # Uncomment the r_sink() commands to log output from stdout/stderr to a file
-        #r_sink(log, type = "message")
         # Load CTL - Should only be done once, since it is quite expensive
         r_library("ctl")
         r_options(stringsAsFactors=False)
-        logger.info("Initialization of CTL done, package loaded in R session")
         # Map the CTLscan function
         self.r_CTLscan = ro.r["CTLscan"]
         # Map the CTLsignificant function
@@ -60,7 +53,6 @@ class CTL:
         self.r_plotCTLobject = ro.r["plot.CTLobject"]
         self.nodes_list = []
         self.edges_list = []
-        logger.info("Obtained pointers to CTL functions")
 
         self.gn2_url = GN2_BRANCH_URL
 
@@ -85,21 +77,12 @@ class CTL:
         self.edges_list.append(edge_dict)
 
     def run_analysis(self, requestform):
-        logger.info("Starting CTL analysis on dataset")
         self.trait_db_list = [trait.strip()
                               for trait in requestform['trait_list'].split(',')]
         self.trait_db_list = [x for x in self.trait_db_list if x]
-
-        logger.debug("strategy:", requestform.get("strategy"))
         strategy = requestform.get("strategy")
-
-        logger.debug("nperm:", requestform.get("nperm"))
         nperm = int(requestform.get("nperm"))
-
-        logger.debug("parametric:", requestform.get("parametric"))
         parametric = bool(requestform.get("parametric"))
-
-        logger.debug("significance:", requestform.get("significance"))
         significance = float(requestform.get("significance"))
 
         # Get the name of the .geno file belonging to the first phenotype
@@ -109,7 +92,6 @@ class CTL:
         genofilelocation = locate(dataset.group.name + ".geno", "genotype")
         parser = genofile_parser.ConvertGenoFile(genofilelocation)
         parser.process_csv()
-        logger.debug("dataset group: ", dataset.group)
         # Create a genotype matrix
         individuals = parser.individuals
         markers = []
@@ -119,8 +101,6 @@ class CTL:
             markers.append(marker["genotypes"])
 
         genotypes = list(itertools.chain(*markers))
-        logger.debug(len(genotypes) / len(individuals),
-                     "==", len(parser.markers))
 
         rGeno = r_t(ro.r.matrix(r_unlist(genotypes), nrow=len(markernames), ncol=len(
             individuals), dimnames=r_list(markernames, individuals), byrow=True))
@@ -128,7 +108,6 @@ class CTL:
         # Create a phenotype matrix
         traits = []
         for trait in self.trait_db_list:
-            logger.debug("retrieving data for", trait)
             if trait != "":
                 ts = trait.split(':')
                 gt = create_trait(name=ts[0], dataset_name=ts[1])
@@ -142,8 +121,6 @@ class CTL:
         rPheno = r_t(ro.r.matrix(r_as_numeric(r_unlist(traits)), nrow=len(self.trait_db_list), ncol=len(
             individuals), dimnames=r_list(self.trait_db_list, individuals), byrow=True))
 
-        logger.debug(rPheno)
-
         # Use a data frame to store the objects
         rPheno = r_data_frame(rPheno, check_names=False)
         rGeno = r_data_frame(rGeno, check_names=False)
@@ -195,8 +172,6 @@ class CTL:
         # Create the interactive graph for cytoscape visualization (Nodes and Edges)
         if not isinstance(significant, ri.RNULLType):
             for x in range(len(significant[0])):
-                logger.debug(significant[0][x], significant[1]
-                             [x], significant[2][x])     # Debug to console
                 # Source
                 tsS = significant[0][x].split(':')
                 # Target
@@ -231,7 +206,6 @@ class CTL:
             n = n + 1
 
     def process_results(self, results):
-        logger.info("Processing CTL output")
         template_vars = {}
         template_vars["results"] = self.results
         template_vars["elements"] = self.elements
diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py
index 938c453e..f52c30e4 100644
--- a/wqflask/wqflask/db_info.py
+++ b/wqflask/wqflask/db_info.py
@@ -6,9 +6,6 @@ import re
 
 from flask import Flask, g
 
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
 
 class InfoPage:
     def __init__(self, start_vars):
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index b0756361..97143486 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -13,10 +13,6 @@ import sys
 from db import webqtlDatabaseFunction
 from utility.tools import GN2_BASE_URL
 
-import logging
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
 
 class DoSearch:
     """Parent class containing parameters/functions used for all searches"""
@@ -41,7 +37,6 @@ class DoSearch:
     def execute(self, query):
         """Executes query and returns results"""
         query = self.normalize_spaces(query)
-        logger.sql(query)
         results = g.db.execute(query, no_parameters=True).fetchall()
         return results
 
@@ -55,7 +50,6 @@ class DoSearch:
     def mescape(self, *items):
         """Multiple escape"""
         escaped = [escape(str(item)) for item in items]
-        logger.debug("escaped is:", escaped)
         return tuple(escaped)
 
     def normalize_spaces(self, stringy):
@@ -69,8 +63,6 @@ class DoSearch:
         if 'key' in search_type and search_type['key'] != None:
             search_type_string += '_' + search_type['key']
 
-        logger.debug("search_type_string is:", search_type_string)
-
         if search_type_string in cls.search_types:
             return cls.search_types[search_type_string]
         else:
@@ -177,8 +169,6 @@ class MrnaAssaySearch(DoSearch):
 
     def run_combined(self, from_clause='', where_clause=''):
         """Generates and runs a combined search of an mRNA expression dataset"""
-
-        logger.debug("Running ProbeSetSearch")
         #query = self.base_query + from_clause + " WHERE " + where_clause
 
         from_clause = self.normalize_spaces(from_clause)
@@ -197,11 +187,8 @@ class MrnaAssaySearch(DoSearch):
 
     def run(self):
         """Generates and runs a simple search of an mRNA expression dataset"""
-
-        logger.debug("Running ProbeSetSearch")
         where_clause = self.get_where_clause()
         query = self.base_query + "WHERE " + where_clause + "ORDER BY ProbeSet.symbol ASC"
-
         return self.execute(query)
 
 
@@ -310,9 +297,6 @@ class PhenotypeSearch(DoSearch):
 
     def run_combined(self, from_clause, where_clause):
         """Generates and runs a combined search of an phenotype dataset"""
-
-        logger.debug("Running PhenotypeSearch")
-
         from_clause = self.normalize_spaces(from_clause)
 
         query = (self.base_query +
@@ -370,7 +354,6 @@ class GenotypeSearch(DoSearch):
             where_clause.append('''%s REGEXP "%s"''' % ("%s.%s" % self.mescape(self.dataset.type,
                                                                                field),
                                                         self.search_term))
-        logger.debug("hello ;where_clause is:", pf(where_clause))
         where_clause = "(%s) " % ' OR '.join(where_clause)
 
         return where_clause
@@ -559,7 +542,6 @@ class LrsSearch(DoSearch):
                                                                        self.species_id)
         else:
             # Deal with >, <, >=, and <=
-            logger.debug("self.search_term is:", self.search_term)
             lrs_val = self.search_term[0]
             if self.search_type == "LOD":
                 lrs_val = lrs_val * 4.61
@@ -794,7 +776,6 @@ class MeanSearch(MrnaAssaySearch):
 
     def run(self):
         self.where_clause = self.get_where_clause()
-        logger.debug("where_clause is:", pf(self.where_clause))
 
         self.query = self.compile_final_query(where_clause=self.where_clause)
 
@@ -824,9 +805,6 @@ class RangeSearch(MrnaAssaySearch):
                                      FROM ProbeSetData
                                      WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s
                                     """ % (escape(self.search_term[0]))
-
-        logger.debug("where_clause is:", pf(where_clause))
-
         return where_clause
 
     def run(self):
@@ -932,11 +910,7 @@ class PvalueSearch(MrnaAssaySearch):
                 self.search_operator,
                 self.search_term[0])
 
-        logger.debug("where_clause is:", pf(self.where_clause))
-
         self.query = self.compile_final_query(where_clause=self.where_clause)
-
-        logger.sql(self.query)
         return self.execute(self.query)
 
 
diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py
index 0a1a597d..9d58162e 100644
--- a/wqflask/wqflask/docs.py
+++ b/wqflask/wqflask/docs.py
@@ -2,9 +2,6 @@ import codecs
 
 from flask import g
 
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
 
 class Docs:
 
diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py
index 0c80e9a4..4b37c7f7 100644
--- a/wqflask/wqflask/export_traits.py
+++ b/wqflask/wqflask/export_traits.py
@@ -14,8 +14,6 @@ from gn3.computations.gemma import generate_hash_of_string
 
 from base.trait import create_trait, retrieve_trait_info
 
-from utility.logger import getLogger
-logger = getLogger(__name__)
 
 def export_traits(targs, export_type):
     if export_type == "collection":
diff --git a/wqflask/wqflask/external_tools/send_to_bnw.py b/wqflask/wqflask/external_tools/send_to_bnw.py
index c1b14ede..dfb59c63 100644
--- a/wqflask/wqflask/external_tools/send_to_bnw.py
+++ b/wqflask/wqflask/external_tools/send_to_bnw.py
@@ -21,9 +21,6 @@
 from base.trait import GeneralTrait
 from utility import helper_functions, corr_result_helpers
 
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
 
 class SendToBNW:
     def __init__(self, start_vars):
diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py
index 9a4f7150..a8066b43 100644
--- a/wqflask/wqflask/external_tools/send_to_geneweaver.py
+++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py
@@ -26,9 +26,6 @@ from base.trait import GeneralTrait, retrieve_trait_info
 from base.species import TheSpecies
 from utility import helper_functions, corr_result_helpers
 
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
 
 class SendToGeneWeaver:
     def __init__(self, start_vars):
diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/wqflask/wqflask/external_tools/send_to_webgestalt.py
index 6e74f4fe..4de684b0 100644
--- a/wqflask/wqflask/external_tools/send_to_webgestalt.py
+++ b/wqflask/wqflask/external_tools/send_to_webgestalt.py
@@ -26,9 +26,6 @@ from base.trait import GeneralTrait, retrieve_trait_info
 from base.species import TheSpecies
 from utility import helper_functions, corr_result_helpers
 
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
 
 class SendToWebGestalt:
     def __init__(self, start_vars):
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 53a124d0..74964297 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -15,9 +15,6 @@ from utility.benchmark import Bench
 from utility.authentication_tools import check_resource_availability
 from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string
 
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
 
 class GSearch:
 
@@ -65,7 +62,6 @@ class GSearch:
                 LIMIT 6000
                 """ % (self.terms)
             with Bench("Running query"):
-                logger.sql(sql)
                 re = g.db.execute(sql).fetchall()
 
             trait_list = []
@@ -210,7 +206,6 @@ class GSearch:
                 ORDER BY Species.`Name`, InbredSet.`Name`, PublishXRef.`Id`
                 LIMIT 6000
                 """.format(group_clause, search_term)
-            logger.sql(sql)
             re = g.db.execute(sql).fetchall()
             trait_list = []
             with Bench("Creating trait objects"):
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index 001bab3b..1c8a4ff6 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -8,12 +8,9 @@ from utility import helper_functions
 from utility.tools import flat_files, REAPER_COMMAND, TEMPDIR
 from redis import Redis
 from flask import Flask, g
-from utility.logger import getLogger
 
 Redis = Redis()
 
-logger = getLogger(__name__)
-
 
 class Heatmap:
 
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 6a62b45c..278d8a6b 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -47,12 +47,11 @@ from wqflask.interval_analyst import GeneUtil
 from base.webqtlConfig import GENERATED_IMAGE_DIR
 from utility.pillow_utils import draw_rotated_text, draw_open_polygon
 
-import utility.logger
+
 try:  # Only import this for Python3
     from functools import reduce
 except:
     pass
-logger = utility.logger.getLogger(__name__)
 
 RED = ImageColor.getrgb("red")
 BLUE = ImageColor.getrgb("blue")
@@ -247,8 +246,6 @@ class DisplayMappingResults:
     HELP_PAGE_REF = '/glossary.html'
 
     def __init__(self, start_vars):
-        logger.info("Running qtlreaper")
-
         self.temp_uuid = start_vars['temp_uuid']
 
         self.dataset = start_vars['dataset']
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 6b525733..646728ba 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -13,8 +13,6 @@ from utility.tools import TEMPDIR
 from utility.tools import WEBSERVER_MODE
 from gn3.computations.gemma import generate_hash_of_string
 
-import utility.logger
-logger = utility.logger.getLogger(__name__)
 
 GEMMAOPTS = "-debug"
 if WEBSERVER_MODE == 'PROD':
diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py
index 2fa80841..75ee189e 100644
--- a/wqflask/wqflask/marker_regression/plink_mapping.py
+++ b/wqflask/wqflask/marker_regression/plink_mapping.py
@@ -5,9 +5,6 @@ from base.webqtlConfig import TMPDIR
 from utility import webqtlUtil
 from utility.tools import flat_files, PLINK_COMMAND
 
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
 
 def run_plink(this_trait, dataset, species, vals, maf):
     plink_output_filename = webqtlUtil.genRandStr(
@@ -15,13 +12,11 @@ def run_plink(this_trait, dataset, species, vals, maf):
     gen_pheno_txt_file(dataset, vals)
 
     plink_command = f"{PLINK_COMMAND}  --noweb --bfile {flat_files('mapping')}/{dataset.group.name} --no-pheno --no-fid --no-parents --no-sex --maf {maf} --out { TMPDIR}{plink_output_filename} --assoc "
-    logger.debug("plink_command:", plink_command)
 
     os.system(plink_command)
 
     count, p_values = parse_plink_output(plink_output_filename, species)
 
-    logger.debug("p_values:", p_values)
     dataset.group.markers.add_pvalues(p_values)
 
     return dataset.group.markers.markers
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index c4b495d7..4d5db2ee 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -10,9 +10,6 @@ from base.trait import GeneralTrait
 from base.data_set import create_dataset
 from utility.tools import flat_files, REAPER_COMMAND, TEMPDIR
 
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
 
 def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boot_check, num_bootstrap, do_control, control_marker, manhattan_plot, first_run=True, output_files=None):
     """Generates p-values for each marker using qtlreaper"""
@@ -67,8 +64,6 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
                               opt_list),
                               webqtlConfig.GENERATED_IMAGE_DIR,
                               output_filename))
-
-        logger.debug("reaper_command:" + reaper_command)
         os.system(reaper_command)
     else:
         output_filename, permu_filename, bootstrap_filename = output_files
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 3bf06ea6..7d112c68 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -17,9 +17,6 @@ from base.webqtlConfig import TMPDIR
 from base.trait import create_trait
 from utility.tools import locate, GN3_LOCAL_URL
 
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
 
 def run_rqtl(trait_name, vals, samples, dataset, pair_scan, mapping_scale, model, method, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, cofactors):
     """Run R/qtl by making a request to the GN3 endpoint and reading in the output file(s)"""
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 35678df9..7a424b17 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -41,9 +41,6 @@ from utility.tools import locate, locate_ignore_error, GEMMA_COMMAND, PLINK_COMM
 from utility.external import shell
 from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR
 
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
 
 class RunMapping:
 
@@ -273,7 +270,6 @@ class RunMapping:
 
             self.control_marker = start_vars['control_marker']
             self.do_control = start_vars['do_control']
-            logger.info("Running qtlreaper")
 
             self.first_run = True
             self.output_files = None
@@ -303,8 +299,6 @@ class RunMapping:
             results = plink_mapping.run_plink(
                 self.this_trait, self.dataset, self.species, self.vals, self.maf)
             #results = self.run_plink()
-        else:
-            logger.debug("RUNNING NOTHING")
 
         self.no_results = False
         if len(results) == 0:
diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py
index 7a808ac9..ddf48d90 100644
--- a/wqflask/wqflask/parser.py
+++ b/wqflask/wqflask/parser.py
@@ -21,9 +21,6 @@ import re
 
 from pprint import pformat as pf
 
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
 
 def parse(pstring):
     """
@@ -45,7 +42,6 @@ def parse(pstring):
 
     for item in pstring:
         splat = re.split(separators, item)
-        logger.debug("splat is:", splat)
 
         # splat is an array of 1 if no match, otherwise more than 1
         if len(splat) > 1:
@@ -73,7 +69,6 @@ def parse(pstring):
                         search_term=[item])
 
         items.append(term)
-    logger.debug("* items are:", pf(items) + "\n")
     return(items)
 
 
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 7134cc24..bf7e3c93 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -25,8 +25,6 @@ from utility.authentication_tools import check_resource_availability
 from utility.tools import GN2_BASE_URL
 from utility.type_checking import is_str
 
-from utility.logger import getLogger
-logger = getLogger(__name__)
 
 class SearchResultPage:
     #maxReturn = 3000
@@ -56,7 +54,6 @@ class SearchResultPage:
         rx = re.compile(
             r'.*\W(href|http|sql|select|update)\W.*', re.IGNORECASE)
         if rx.match(search):
-            logger.debug("Regex failed search")
             self.search_term_exists = False
             return
         else:
diff --git a/wqflask/wqflask/update_search_results.py b/wqflask/wqflask/update_search_results.py
index 2e467dc8..6b1b4e97 100644
--- a/wqflask/wqflask/update_search_results.py
+++ b/wqflask/wqflask/update_search_results.py
@@ -7,9 +7,6 @@ from db import webqtlDatabaseFunction
 
 from utility.benchmark import Bench
 
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
 
 class GSearch:
 
@@ -47,7 +44,6 @@ class GSearch:
                 LIMIT 6000
                 """ % (self.terms)
             with Bench("Running query"):
-                logger.sql(sql)
                 re = g.db.execute(sql).fetchall()
             self.trait_list = []
             with Bench("Creating trait objects"):
@@ -92,7 +88,6 @@ class GSearch:
                 ORDER BY Species.`Name`, InbredSet.`Name`, PublishXRef.`Id`
                 LIMIT 6000
                 """ % (self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms)
-            logger.sql(sql)
             re = g.db.execute(sql).fetchall()
             self.trait_list = []
             with Bench("Creating trait objects"):
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index 45a12f77..ae61edb0 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -2,7 +2,6 @@ import os
 import hashlib
 import datetime
 import time
-import logging
 import uuid
 import hmac
 import base64
@@ -21,9 +20,6 @@ from utility import hmac
 from utility.redis_tools import is_redis_available, get_redis_conn, get_user_id, get_user_by_unique_column, set_user_attribute, save_user, save_verification_code, check_verification_code, get_user_collections, save_collections
 Redis = get_redis_conn()
 
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
 from smtplib import SMTP
 from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD, LOG_SQL_ALCHEMY, GN2_BRANCH_URL
 
@@ -129,7 +125,6 @@ def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
         server.login(SMTP_USERNAME, SMTP_PASSWORD)
         server.sendmail(fromaddr, toaddr, msg)
         server.quit()
-    logger.info("Successfully sent email to " + toaddr)
 
 
 def send_verification_email(user_details, template_name="email/user_verification.txt", key_prefix="verification_code", subject="GeneNetwork e-mail verification"):
@@ -346,7 +341,6 @@ def get_github_user_details(access_token):
 
 @app.route("/n/logout")
 def logout():
-    logger.debug("Logging out...")
     UserSession().delete_session()
     flash("You are now logged out. We hope you come back soon!")
     response = make_response(redirect(url_for('index_page')))
@@ -404,7 +398,6 @@ def forgot_password_submit():
     email_address = params['email_address']
     next_page = None
     if email_address != "":
-        logger.debug("Wants to send password E-mail to ", email_address)
         user_details = get_user_by_unique_column(
             "email_address", email_address)
         if user_details:
@@ -425,8 +418,6 @@ def forgot_password_submit():
 @app.route("/n/password_reset", methods=['GET'])
 def password_reset():
     """Entry point after user clicks link in E-mail"""
-    logger.debug("in password_reset request.url is:", request.url)
-
     verification_code = request.args.get('code')
     hmac = request.args.get('hm')
 
@@ -446,8 +437,6 @@ def password_reset():
 @app.route("/n/password_reset_step2", methods=('POST',))
 def password_reset_step2():
     """Handle confirmation E-mail for password reset"""
-    logger.debug("in password_reset request.url is:", request.url)
-
     errors = []
     user_email = request.form['user_encode']
     user_id = get_user_id("email_address", user_email)
@@ -515,7 +504,6 @@ def register():
     params = params.to_dict(flat=True)
 
     if params:
-        logger.debug("Attempting to register the user...")
         errors = register_user(params)
 
         if len(errors) == 0:
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index 00b268a7..1ed5b802 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -13,8 +13,6 @@ from utility import hmac
 from utility.redis_tools import get_redis_conn, get_user_id, get_user_by_unique_column, set_user_attribute, get_user_collections, save_collections
 Redis = get_redis_conn()
 
-from utility.logger import getLogger
-logger = getLogger(__name__)
 
 THREE_DAYS = 60 * 60 * 24 * 3
 THIRTY_DAYS = 60 * 60 * 24 * 30
@@ -54,7 +52,6 @@ def create_signed_cookie():
     the_uuid = str(uuid.uuid4())
     signature = hmac.hmac_creation(the_uuid)
     uuid_signed = the_uuid + ":" + signature
-    logger.debug("uuid_signed:", uuid_signed)
     return the_uuid, uuid_signed